# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 05:43:21 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N~6~-(3,4-dimethoxyphenyl)-2-(morpholin-4-yl)-4,5'-bipyrimidine-2',6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Nc2cc(nc(n2)N3CCOCC3)c4cnc(N)nc4)cc1OC
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 13K  13K  N~6~-(3,4-dimethoxyphenyl)-2-(morpholin-4-yl)-4,5'-bipyrimidine-2',6-diamine  ligand  53  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_13K
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 13K  N01   N  NH2   0  -0.793   7.6982   1.9234  -0.0231
 13K  C02   C  CR6   0   0.573   6.4129   1.5524   0.0055
 13K  N03   N  N     0  -0.444   6.1488   0.2397   0.0679
 13K  C04   C  CR16  0   0.003   4.8783  -0.1076   0.0827
 13K  N05   N  N     0  -0.447   5.4891   2.5228  -0.0444
 13K  C06   C  CR16  0  -0.020   4.2289   2.1415  -0.0259
 13K  C07   C  CR6   0  -0.120   3.8268   0.8086   0.0401
 13K  C08   C  CR6   0   0.338   2.4235   0.3751   0.0705
 13K  C09   C  CR16  0  -0.506   1.3746   1.2730   0.0899
 13K  N10   N  N     0  -0.547   2.2220  -0.9460   0.0867
 13K  C11   C  CR6   0   0.657   0.9609  -1.3674   0.1184
 13K  N12   N  NT    0  -0.518   0.7476  -2.7069   0.0936
 13K  C13   C  CH2   0  -0.308  -0.5666  -3.2893   0.2754
 13K  C14   C  CH2   0  -0.165  -0.7267  -4.4874  -0.6431
 13K  O15   O  O2    0  -0.480   0.3065  -5.4303  -0.4636
 13K  C16   C  CH2   0  -0.167   1.5667  -4.8461  -0.7073
 13K  C17   C  CH2   0  -0.305   1.8296  -3.6641   0.2078
 13K  N18   N  N     0  -0.535  -0.1221  -0.5846   0.1597
 13K  C19   C  CR6   0   0.600   0.0811   0.7218   0.1388
 13K  N20   N  NH1   0  -0.779  -0.9807   1.5678   0.1641
 13K  C21   C  CR6   0   0.390  -2.3504   1.2935   0.2204
 13K  C22   C  CR16  0  -0.310  -2.9045   0.1335   0.7367
 13K  C23   C  CR16  0  -0.358  -4.2914  -0.0140   0.7755
 13K  C24   C  CR16  0  -0.483  -3.2051   2.3043  -0.2456
 13K  C25   C  CR6   0   0.335  -4.5790   2.1624  -0.1940
 13K  O26   O  O2    0  -0.461  -5.4590   3.0891  -0.6147
 13K  C27   C  CH3   0  -0.403  -4.9579   4.3061  -1.1296
 13K  C28   C  CR6   0   0.305  -5.1408   0.9765   0.3213
 13K  O29   O  O2    0  -0.450  -6.4887   0.9166   0.3263
 13K  C30   C  CH3   0  -0.409  -7.0948  -0.2305   0.8836
 13K  HN01  H  HNH2  0   0.386   7.9429   2.8970   0.0220
 13K  HN0A  H  HNH2  0   0.381   8.4223   1.2406   0.1131
 13K  H04   H  HCR6  0   0.263   4.6666  -1.1693   0.1336
 13K  H06   H  HCR6  0   0.231   3.4991   2.9432  -0.0652
 13K  H09   H  HCR6  0   0.219   1.5133   2.3443   0.0822
 13K  H13   H  HCH2  0   0.220  -0.7020  -3.5958   1.3206
 13K  H13A  H  HCH2  0   0.272  -1.3344  -2.5553   0.0453
 13K  H14   H  HCH2  0   0.229  -1.6716  -4.9897  -0.4316
 13K  H14A  H  HCH2  0   0.197  -0.7519  -4.1396  -1.6855
 13K  H16   H  HCH2  0   0.229   2.3226  -5.6146  -0.5402
 13K  H16A  H  HCH2  0   0.196   1.6429  -4.5177  -1.7535
 13K  H17   H  HCH2  0   0.270   2.7704  -3.1949  -0.0664
 13K  H17A  H  HCH2  0   0.221   1.9184  -4.0082   1.2461
 13K  HN20  H  HNH1  0   0.378  -0.7481   2.5418   0.0491
 13K  H22   H  HCR6  0   0.268  -2.2830  -0.6605   1.1157
 13K  H23   H  HCR6  0   0.253  -4.6869  -0.9348   1.1803
 13K  H24   H  HCR6  0   0.254  -2.7665   3.2063  -0.6527
 13K  H27   H  HCH3  0   0.213  -4.3574   4.8455  -0.3922
 13K  H27A  H  HCH3  0   0.217  -4.3564   4.1532  -2.0296
 13K  H27B  H  HCH3  0   0.249  -5.8234   4.9112  -1.3877
 13K  H30   H  HCH3  0   0.209  -6.8308  -1.1408   0.3380
 13K  H30A  H  HCH3  0   0.210  -6.8279  -0.3631   1.9360
 13K  H30B  H  HCH3  0   0.245  -8.1693  -0.0801   0.8106

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 13K  N01  C02   single    1.338  0.020  1.338
 13K  N01  HN01  single    0.860  0.020  1.020
 13K  N01  HN0A  single    0.860  0.020  1.020
 13K  N03  C02   aromatic  1.340  0.020  1.340
 13K  C02  N05   aromatic  1.341  0.020  1.341
 13K  N03  C04   aromatic  1.317  0.020  1.317
 13K  C04  C07   aromatic  1.395  0.020  1.395
 13K  C04  H04   single    0.930  0.020  1.080
 13K  N05  C06   aromatic  1.317  0.020  1.317
 13K  C07  C06   aromatic  1.394  0.020  1.394
 13K  C06  H06   single    0.930  0.020  1.080
 13K  C07  C08   single    1.469  0.020  1.469
 13K  C09  C08   aromatic  1.381  0.020  1.381
 13K  C08  N10   aromatic  1.336  0.020  1.336
 13K  C09  C19   aromatic  1.407  0.020  1.407
 13K  C09  H09   single    0.930  0.020  1.080
 13K  N10  C11   aromatic  1.330  0.020  1.330
 13K  N18  C11   aromatic  1.337  0.020  1.337
 13K  C11  N12   single    1.357  0.020  1.357
 13K  N12  C13   single    1.449  0.020  1.449
 13K  N12  C17   single    1.449  0.020  1.449
 13K  C13  C14   single    1.518  0.020  1.518
 13K  C13  H13   single    0.970  0.020  1.090
 13K  C13  H13A  single    0.970  0.020  1.090
 13K  C14  O15   single    1.410  0.020  1.410
 13K  C14  H14   single    0.970  0.020  1.090
 13K  C14  H14A  single    0.970  0.020  1.090
 13K  O15  C16   single    1.410  0.020  1.410
 13K  C17  C16   single    1.518  0.020  1.518
 13K  C16  H16   single    0.970  0.020  1.090
 13K  C16  H16A  single    0.970  0.020  1.090
 13K  C17  H17   single    0.970  0.020  1.090
 13K  C17  H17A  single    0.970  0.020  1.090
 13K  C19  N18   aromatic  1.322  0.020  1.322
 13K  N20  C19   single    1.358  0.020  1.358
 13K  N20  C21   single    1.398  0.020  1.398
 13K  N20  HN20  single    0.860  0.020  1.020
 13K  C24  C21   aromatic  1.403  0.020  1.403
 13K  C21  C22   aromatic  1.385  0.020  1.385
 13K  C22  C23   aromatic  1.395  0.020  1.395
 13K  C22  H22   single    0.930  0.020  1.080
 13K  C28  C23   aromatic  1.382  0.020  1.382
 13K  C23  H23   single    0.930  0.020  1.080
 13K  C24  C25   aromatic  1.382  0.020  1.382
 13K  C24  H24   single    0.930  0.020  1.080
 13K  O26  C25   single    1.345  0.020  1.345
 13K  C25  C28   aromatic  1.410  0.020  1.410
 13K  C27  O26   single    1.413  0.020  1.413
 13K  C27  H27   single    0.970  0.020  1.090
 13K  C27  H27A  single    0.970  0.020  1.090
 13K  C27  H27B  single    0.970  0.020  1.090
 13K  C28  O29   single    1.349  0.020  1.349
 13K  O29  C30   single    1.412  0.020  1.412
 13K  C30  H30   single    0.970  0.020  1.090
 13K  C30  H30A  single    0.970  0.020  1.090
 13K  C30  H30B  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 13K  HN0A  N01  HN01  118.49  3.000
 13K  HN0A  N01  C02   120.07  3.000
 13K  HN01  N01  C02   120.10  3.000
 13K  N05   C02  N03   125.09  3.000
 13K  N05   C02  N01   117.41  3.000
 13K  N03   C02  N01   117.50  3.000
 13K  C04   N03  C02   116.66  3.000
 13K  H04   C04  C07   119.84  3.000
 13K  H04   C04  N03   116.56  3.000
 13K  C07   C04  N03   123.60  3.000
 13K  C06   N05  C02   116.70  3.000
 13K  H06   C06  C07   120.95  3.000
 13K  H06   C06  N05   115.42  3.000
 13K  C07   C06  N05   123.62  3.000
 13K  C08   C07  C06   123.97  3.000
 13K  C08   C07  C04   121.70  3.000
 13K  C06   C07  C04   114.33  3.000
 13K  N10   C08  C09   121.88  3.000
 13K  N10   C08  C07   115.85  3.000
 13K  C09   C08  C07   122.28  3.000
 13K  H09   C09  C19   120.45  3.000
 13K  H09   C09  C08   123.18  3.000
 13K  C19   C09  C08   116.36  3.000
 13K  C11   N10  C08   117.16  3.000
 13K  N18   C11  N12   116.83  3.000
 13K  N12   C11  N10   117.49  3.000
 13K  N18   C11  N10   125.68  3.000
 13K  C17   N12  C13   113.70  3.000
 13K  C17   N12  C11   122.23  3.000
 13K  C13   N12  C11   122.49  3.000
 13K  H13A  C13  H13   107.64  3.000
 13K  H13A  C13  C14   109.29  3.000
 13K  H13   C13  C14   110.04  3.000
 13K  H13A  C13  N12   110.05  3.000
 13K  H13   C13  N12   110.10  3.000
 13K  C14   C13  N12   109.69  3.000
 13K  H14A  C14  H14   108.04  3.000
 13K  H14A  C14  O15   110.43  3.000
 13K  H14   C14  O15   107.58  3.000
 13K  H14A  C14  C13   109.05  3.000
 13K  H14   C14  C13   109.72  3.000
 13K  O15   C14  C13   111.93  3.000
 13K  C16   O15  C14   110.84  3.000
 13K  H16A  C16  H16   107.96  3.000
 13K  H16A  C16  C17   109.22  3.000
 13K  H16   C16  C17   109.65  3.000
 13K  H16A  C16  O15   110.50  3.000
 13K  H16   C16  O15   107.51  3.000
 13K  C17   C16  O15   111.91  3.000
 13K  H17A  C17  H17   107.70  3.000
 13K  H17A  C17  C16   109.89  3.000
 13K  H17   C17  C16   109.52  3.000
 13K  H17A  C17  N12   110.01  3.000
 13K  H17   C17  N12   109.96  3.000
 13K  C16   C17  N12   109.73  3.000
 13K  C19   N18  C11   116.97  3.000
 13K  N20   C19  N18   119.67  3.000
 13K  N20   C19  C09   118.39  3.000
 13K  N18   C19  C09   121.93  3.000
 13K  HN20  N20  C21   114.85  3.000
 13K  HN20  N20  C19   114.80  3.000
 13K  C21   N20  C19   130.14  3.000
 13K  C24   C21  C22   118.90  3.000
 13K  C22   C21  N20   124.83  3.000
 13K  C24   C21  N20   116.24  3.000
 13K  H22   C22  C23   119.07  3.000
 13K  H22   C22  C21   121.16  3.000
 13K  C23   C22  C21   119.77  3.000
 13K  H23   C23  C28   120.60  3.000
 13K  H23   C23  C22   117.66  3.000
 13K  C28   C23  C22   121.75  3.000
 13K  H24   C24  C25   120.16  3.000
 13K  H24   C24  C21   118.57  3.000
 13K  C25   C24  C21   121.27  3.000
 13K  C28   C25  O26   115.66  3.000
 13K  C28   C25  C24   119.75  3.000
 13K  O26   C25  C24   124.59  3.000
 13K  C27   O26  C25   118.37  3.000
 13K  H27B  C27  H27A  108.69  3.000
 13K  H27B  C27  H27   108.83  3.000
 13K  H27A  C27  H27   108.79  3.000
 13K  H27B  C27  O26   106.47  3.000
 13K  H27A  C27  O26   112.00  3.000
 13K  H27   C27  O26   111.95  3.000
 13K  O29   C28  C25   115.90  3.000
 13K  O29   C28  C23   125.53  3.000
 13K  C25   C28  C23   118.57  3.000
 13K  C30   O29  C28   117.80  3.000
 13K  H30B  C30  H30A  108.81  3.000
 13K  H30B  C30  H30   108.67  3.000
 13K  H30A  C30  H30   108.68  3.000
 13K  H30B  C30  O29   106.58  3.000
 13K  H30A  C30  O29   111.93  3.000
 13K  H30   C30  O29   112.06  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 13K  CONST_01  C07   C04  N03  C02     0.00   0.0  0
 13K  CONST_02  C07   C06  N05  C02     0.00   0.0  0
 13K  CONST_03  C06   N05  C02  N03     0.00   0.0  0
 13K  CONST_04  C06   C07  C04  N03     0.00   0.0  0
 13K  CONST_05  C08   C07  C04  N03   180.00   0.0  0
 13K  CONST_06  N05   C02  N03  C04     0.00   0.0  0
 13K  CONST_07  N05   C06  C07  C04     0.00   0.0  0
 13K  CONST_08  C09   C08  C07  C04   180.00   0.0  0
 13K  CONST_09  N10   C08  C07  C04     0.00   0.0  0
 13K  CONST_10  C08   C07  C06  N05   180.00   0.0  0
 13K  CONST_11  C09   C08  C07  C06     0.00   0.0  0
 13K  CONST_12  N10   C08  C07  C06   180.00   0.0  0
 13K  CONST_13  C19   C09  C08  C07   180.00   0.0  0
 13K  CONST_14  C11   N10  C08  C07   180.00   0.0  0
 13K  CONST_15  N18   C19  C09  C08     0.00   0.0  0
 13K  CONST_16  N18   C11  N10  C08     0.00   0.0  0
 13K  CONST_17  C11   N10  C08  C09     0.00   0.0  0
 13K  CONST_18  C11   N18  C19  C09     0.00   0.0  0
 13K  CONST_19  C19   C09  C08  N10     0.00   0.0  0
 13K  CONST_20  C19   N18  C11  N10     0.00   0.0  0
 13K  CONST_21  C28   C25  C24  C21     0.00   0.0  0
 13K  CONST_22  C28   C23  C22  C21     0.00   0.0  0
 13K  CONST_23  C25   C24  C21  C22     0.00   0.0  0
 13K  CONST_24  C25   C28  C23  C22     0.00   0.0  0
 13K  CONST_25  C24   C21  C22  C23     0.00   0.0  0
 13K  CONST_26  C24   C25  C28  C23     0.00   0.0  0
 13K  CONST_27  N12   C11  N10  C08   180.00   0.0  0
 13K  CONST_28  C19   N18  C11  N12   180.00   0.0  0
 13K  CONST_29  C04   N03  C02  N01   180.00   0.0  0
 13K  CONST_30  C06   N05  C02  N01   180.00   0.0  0
 13K  CONST_31  N20   C19  C09  C08   180.00   0.0  0
 13K  CONST_32  N20   C19  N18  C11   180.00   0.0  0
 13K  CONST_33  C25   C24  C21  N20   180.00   0.0  0
 13K  CONST_34  C23   C22  C21  N20   180.00   0.0  0
 13K  CONST_35  O26   C25  C24  C21   180.00   0.0  0
 13K  CONST_36  O29   C28  C23  C22   180.00   0.0  0
 13K  CONST_37  O26   C25  C28  C23   180.00   0.0  0
 13K  CONST_38  O29   C28  C25  C24   180.00   0.0  0
 13K  CONST_39  H04   C04  N03  C02   180.00   0.0  0
 13K  CONST_40  H06   C06  N05  C02   180.00   0.0  0
 13K  CONST_41  H09   C09  C08  C07     0.00   0.0  0
 13K  CONST_42  H23   C23  C22  C21   180.00   0.0  0
 13K  CONST_43  H24   C24  C21  C22   180.00   0.0  0
 13K  CONST_44  H22   C22  C21  C24   180.00   0.0  0
 13K  CONST_45  HN01  N01  C02  N03   180.00   0.0  0
 13K  CONST_46  HN0A  N01  C02  N03     0.00   0.0  0
 13K  Var_01    C13   N12  C11  N10   172.86  30.0  2
 13K  Var_02    C14   C13  N12  C11   142.01  30.0  1
 13K  Var_03    C16   C17  N12  C11  -141.97  30.0  1
 13K  Var_04    O15   C14  C13  N12    54.63  30.0  1
 13K  Var_05    O15   C16  C17  N12   -54.59  30.0  1
 13K  Var_06    C17   C16  O15  C14    58.75  30.0  1
 13K  Var_07    C21   N20  C19  C09  -179.56  30.0  3
 13K  Var_08    C24   C21  N20  C19  -157.58  30.0  2
 13K  Var_09    C28   C25  O26  C27   179.37  30.0  2
 13K  Var_10    H27   C27  O26  C25   -60.00  30.0  3
 13K  Var_11    H30   C30  O29  C28   -62.29  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 13K  plan-1  N01   0.020
 13K  plan-1  C02   0.020
 13K  plan-1  N03   0.020
 13K  plan-1  C04   0.020
 13K  plan-1  N05   0.020
 13K  plan-1  C06   0.020
 13K  plan-1  C07   0.020
 13K  plan-1  C08   0.020
 13K  plan-1  H04   0.020
 13K  plan-1  H06   0.020
 13K  plan-2  C07   0.020
 13K  plan-2  C08   0.020
 13K  plan-2  C09   0.020
 13K  plan-2  N10   0.020
 13K  plan-2  C11   0.020
 13K  plan-2  N12   0.020
 13K  plan-2  N18   0.020
 13K  plan-2  C19   0.020
 13K  plan-2  N20   0.020
 13K  plan-2  H09   0.020
 13K  plan-3  N20   0.020
 13K  plan-3  C21   0.020
 13K  plan-3  C22   0.020
 13K  plan-3  C23   0.020
 13K  plan-3  C24   0.020
 13K  plan-3  C25   0.020
 13K  plan-3  O26   0.020
 13K  plan-3  C28   0.020
 13K  plan-3  O29   0.020
 13K  plan-3  H22   0.020
 13K  plan-3  H23   0.020
 13K  plan-3  H24   0.020
 13K  plan-4  N01   0.020
 13K  plan-4  C02   0.020
 13K  plan-4  HN01  0.020
 13K  plan-4  HN0A  0.020

